Week 2 Protein Degradation Module

Question 1

What is the functional difference between proteins with long life spans and proteins with relatively short lifespans?

Answer 1

Long lived proteins: may be involved with structure of the cell

Short lived proteins: need to respond quickly to change and are likely part of metabolic processes, cell signaling, or cell division

Question 2

Define Proteolysis

Answer 2

breakdown of proteins into peptide fragments and AAs

Question 3

Define proteases

Answer 3

the enzymes responsible for the breakdown of proteins

Question 4

What are the two pathways of protein degradation?

Answer 4

ubiquitin-proteasome pathway, lysosomal pathway

Question 5

describe the ubiquitin-proteasome pathway: general pathway? what does it degrade? does it require energy?

Answer 5

General pathway: proteins are marked with a chaing of ubiquitin molecules and then degraded by proteasomes

A selective process that degrades short-lived, damaged or misfolded proteins.

Requires ATP

Question 6

What enzymes are involved in ubiquination of proteins?

Answer 6

E1
E2
E3

Question 7

At what points is ATP needed for the ubiquitin-proteasome pathway?

Answer 7

ATP is needed to attach Ub to E1. and ATP is needed during the breakdown of proteins with proteasome

Question 8

Describe how the enzymes work in the ubiquitin-proteasome pathway

Answer 8

Ub attaches to E1 (ATP is hydrolyzed)–>E1-Ub transfers its Ub to E2–>E3 ligase transfers Ub to the target protein

Question 9

After a Ub tagged protein is degraded, what happens to attacehd Ub?

Answer 9

they are recylced

Question 10

What is the general structure of a proteasome?

Answer 10

contain an inner active site (protein degradation) and out protein binding sites.

Question 11

compare the relative number of different E3 and E1 enzymes?

Answer 11

the genome has >600 Ub E3 ligases and much fewer E1 enzymes.

Question 12

How do cytosolic proteins enter a lysosome?

Answer 12

Autophagy!

Question 13

What are the three types of Autophagy?

Answer 13

Macroautophagy, microautophagy, chaperone-mediated autophagy

Question 14

What types of things are consume with macroautophagy? (3)

Answer 14

proteins, protein aggregates, mitochondrium (organelles)

Question 15

Describe the process/steps of macroautophagy

Answer 15

an isolation membrane (double membrane) expands to engulf cytosolic cargo–>cargo is sequestered in autophagosome (closed isolation membrane)–>autophagosome fuses with lysosome and contents are degraded

Question 16

Describe the steps of microautophagy

Answer 16

lysosome invaginates and directly eats cytosolic components

Question 17

What is an autophagic tube? where is it seen?

Answer 17

the invagination of the lysosome seen during the process of microautophagy. Vesicles bud off the tube and into the lysosome.

Question 18

describe the selectivity of macroautophagy, microautophagy, and chaperone-mediated autophagy

Answer 18

micro and macro: can be random or selective.

Chaperone: highly selective

Question 19

what types of proteins are degraded by chaperone-mediated autophagy?

Answer 19

long-lived dispensable proteins (contrasts to Ub-mediated that degrades short lived)

Question 20

what motif targets proteins to chaperone-mediated autophagy?

Answer 20

KFEQR motif

Question 21

what are the steps of chaperone-mediated autophagy

Answer 21

Protein with KFEQR motif binds chaperone in cytosol–>chaperone targets protein to lysosomal membrane–>protein binds LAMP2A on surface of lysosomal membrane–>LAMP2A translocates protein into lysosomal lumen

Question 22

what induces autophagy?

Answer 22

cellular stress

Question 23

In general, what type of proteins are targeted by Ub-proteasome pathway and Autophagy? Selectivity?

Answer 23

Autophagy: long lived proteins and organelles (selective or non-selective)

Ub-Proteasome: short lived, damaged, or misfolded proteins. highly selective

Question 24

what is mTOR? what does it do? during cell stress?

Answer 24

mTOR is a master regulator that positively promotes cell growth and proliferation. in a healthy cell mTOR inhibits expression of autophagy related genes. Under cellular stress mTOR signaling is impaired and Atgs are upregulated